Four Afghan civilians were mistakenly killed and two others injured in an attack by a remotely controlled RAF "drone" targeting insurgent leaders in Helmand province, the Guardian has learned.

The airstrike marks the first confirmed operation in which one of the UK's Reaper aircraft has been responsible for the deaths of civilians, and comes amid growing concern on both sides of the Atlantic about increased use of drones in combat zones.

The revelation may also complicate the task of British commanders in the province as they try to secure the trust of local people ahead of "transition" – the symbolic moment later this month when Afghan forces take the lead for security in areas currently under UK control.

However, the British military remain convinced about the use of Reapers and insist the civilian deaths were due to intelligence failures on the ground rather than problems with the aircraft. Military officials have told the Guardian it is possible that almost one third of the RAF could be made up of remotely controlled aircraft within 20 years, such is the confidence in their capability.

The airstrike that caused the civilian casualties was meant to kill a Taliban commander who was being tracked on the ground in the Now Zad district of north Helmand. According to sources, the leader was correctly identified and the Reaper, which was flying close by, was instructed to attack. The Reaper pilots were thousands of miles away at a US Airforce base in Nevada when they were given the all clear to fire on two trucks.

Both vehicles were destroyed – at least one of them is thought to have been packed with explosive. An insurgent commander and an associate were killed, but it soon became clear that civilians were also in the vehicles.

"It was extremely unfortunate that the civilians were killed," said a Whitehall source. "The attack would not have taken place if we had known that there were civilians in the vehicles as well."

The incident took place on 25 March this year and an inquiry was launched by investigators from the International Security Assistance Force (ISAF).

ISAF confirmed that "civilians were discovered in the vehicles following the airstrike during a battle damage assessment"; this was conducted by soldiers sent to confirm what had happened.

"This is the first case when civilian deaths have been caused by one of our Reapers," said the source. "There has been a comprehensive investigation to ensure it doesn't happen again."

A Ministry of Defence spokesman said: "Any incident involving civilian casualties is a matter of deep regret and we take every possible measure to avoid such incidents. On 25 March a UK Reaper was tasked to engage and destroy two pick up trucks. The strike resulted in the deaths of two insurgents and the destruction of a significant quantity of explosives being carried on the trucks. Sadly, four Afghan civilians were also killed and a further two Afghan civilians were injured. There are strict procedures, frequently updated in light of experience, intended to both minimise the risk of casualties occurring and to investigate any incidents that do happen.

"An ISAF investigation was conducted to establish if any lessons could be learnt from the incident or if errors in operational procedures could be identified; the report noted that the UK Reaper's crews actions had been in accordance with procedures and UK Rules of Engagement."

The families of the civilian victims will be entitled to compensation if they report to a British base and can prove their identity.

Chris Cole, a campaigner who runs the Drone Wars UK website, which monitors the development of unmanned weapons systems, said he was concerned at the time it took for the attack to be made public.

"The secrecy and lack of accountability surrounding the use of British armed drones is a matter of great concern. There needs to be a full and public investigation of all the issues raised by the increasing use of armed unmanned drones by British forces."

The RAF has been piloting Reapers from Creech Air Force base in Nevada since late 2007. The MoD bought the aircraft as an "urgent operational requirement" to help in the fight against the Taliban. Since then the Reapers have flown a total of 23,400 hours and fired 176 missiles and laser guided bombs. Last year David Cameron said 124 insurgents had been killed by UK drones during their Afghan deployment.

The RAF's leading expert on Reapers, Wing Commander Chris Thirtle, told the Guardian some pilots in the future may never have to actually fly aircraft, beyond their initial training. Instead, they will be trained to use remote controlled aircraft for combat missions.

Most of the concern about drones has centred on their extensive use by the CIA and American military commanders to attack al-Qaida commanders in Pakistan. Some studies have estimated that hundreds of civilians have also been killed in these strikes.

In 2009 an RAF drone fired on suspected insurgents in Sangin, helping Royal Marines who were patrolling in the area. The attack is thought to have injured two children, who were flown to the British base at Camp Bastion for treatment.